Structure

Physi-Chem Properties

Molecular Weight:  284.18
Volume:  333.669
LogP:  5.892
LogD:  3.628
LogS:  -6.159
# Rotatable Bonds:  10
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.278
Synthetic Accessibility Score:  3.073
Fsp3:  0.526
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.131
MDCK Permeability:  5.313391739036888e-05
Pgp-inhibitor:  0.147
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.147
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.31488800048828%
Volume Distribution (VD):  1.488
Pgp-substrate:  1.0379939079284668%

ADMET: Metabolism

CYP1A2-inhibitor:  0.942
CYP1A2-substrate:  0.406
CYP2C19-inhibitor:  0.864
CYP2C19-substrate:  0.449
CYP2C9-inhibitor:  0.87
CYP2C9-substrate:  0.985
CYP2D6-inhibitor:  0.1
CYP2D6-substrate:  0.493
CYP3A4-inhibitor:  0.831
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  6.969
Half-life (T1/2):  0.208

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.114
Drug-inuced Liver Injury (DILI):  0.969
AMES Toxicity:  0.441
Rat Oral Acute Toxicity:  0.065
Maximum Recommended Daily Dose:  0.097
Skin Sensitization:  0.977
Carcinogencity:  0.58
Eye Corrosion:  0.974
Eye Irritation:  0.963
Respiratory Toxicity:  0.74

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC161366

Natural Product ID:  NPC161366
Common Name*:   Methyloropheate
IUPAC Name:   methyl octadec-17-en-9,11,13-triynoate
Synonyms:   Methyloropheate
Standard InCHIKey:  PKNRJGAFIWZODZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C19H24O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19(20)21-2/h3H,1,4-5,12-18H2,2H3
SMILES:  C=CCCC#CC#CC#CCCCCCCCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1080661
PubChem CID:   44606074
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters
          • [CHEMONTID:0003417] Fatty acid methyl esters

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota stem bark n.a. n.a. PMID[19874044]
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC = 50.0 ug.mL-1 PMID[475016]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 12.0 ug.mL-1 PMID[475016]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 25.0 ug.mL-1 PMID[475016]
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 25.0 ug.mL-1 PMID[475016]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC161366 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9167 High Similarity NPC216130
0.8824 High Similarity NPC18357
0.8654 High Similarity NPC139545
0.8654 High Similarity NPC39633
0.8654 High Similarity NPC309606
0.8627 High Similarity NPC470412
0.8627 High Similarity NPC470410
0.8519 High Similarity NPC187777
0.8519 High Similarity NPC179764
0.8431 Intermediate Similarity NPC224227
0.8333 Intermediate Similarity NPC54766
0.8333 Intermediate Similarity NPC223677
0.8333 Intermediate Similarity NPC128061
0.8333 Intermediate Similarity NPC28779
0.8333 Intermediate Similarity NPC200845
0.8333 Intermediate Similarity NPC274290
0.8333 Intermediate Similarity NPC10316
0.8333 Intermediate Similarity NPC473863
0.8333 Intermediate Similarity NPC228473
0.8302 Intermediate Similarity NPC71761
0.8269 Intermediate Similarity NPC262968
0.8039 Intermediate Similarity NPC180534
0.8036 Intermediate Similarity NPC225929
0.8 Intermediate Similarity NPC474672
0.7963 Intermediate Similarity NPC294548
0.7963 Intermediate Similarity NPC139029
0.7963 Intermediate Similarity NPC36061
0.7963 Intermediate Similarity NPC1813
0.7818 Intermediate Similarity NPC290563
0.7818 Intermediate Similarity NPC87564
0.7818 Intermediate Similarity NPC32467
0.7818 Intermediate Similarity NPC88966
0.7818 Intermediate Similarity NPC154245
0.7818 Intermediate Similarity NPC281972
0.7818 Intermediate Similarity NPC6095
0.7818 Intermediate Similarity NPC85813
0.7818 Intermediate Similarity NPC424
0.7818 Intermediate Similarity NPC25417
0.7818 Intermediate Similarity NPC261831
0.7778 Intermediate Similarity NPC281245
0.7778 Intermediate Similarity NPC310746
0.7636 Intermediate Similarity NPC70387
0.7636 Intermediate Similarity NPC321062
0.7627 Intermediate Similarity NPC229252
0.7627 Intermediate Similarity NPC45097
0.7627 Intermediate Similarity NPC235242
0.7627 Intermediate Similarity NPC143857
0.7593 Intermediate Similarity NPC28205
0.7593 Intermediate Similarity NPC284212
0.7586 Intermediate Similarity NPC267817
0.7547 Intermediate Similarity NPC207815
0.7547 Intermediate Similarity NPC250919
0.7544 Intermediate Similarity NPC18951
0.7544 Intermediate Similarity NPC477201
0.7541 Intermediate Similarity NPC470320
0.7541 Intermediate Similarity NPC226592
0.75 Intermediate Similarity NPC201939
0.7455 Intermediate Similarity NPC92114
0.7377 Intermediate Similarity NPC54925
0.7368 Intermediate Similarity NPC477984
0.7347 Intermediate Similarity NPC28598
0.7347 Intermediate Similarity NPC161097
0.7333 Intermediate Similarity NPC243532
0.7292 Intermediate Similarity NPC305660
0.7292 Intermediate Similarity NPC22903
0.7292 Intermediate Similarity NPC201622
0.7292 Intermediate Similarity NPC54980
0.7288 Intermediate Similarity NPC469373
0.7273 Intermediate Similarity NPC470411
0.7258 Intermediate Similarity NPC328089
0.7258 Intermediate Similarity NPC68343
0.7255 Intermediate Similarity NPC255837
0.7255 Intermediate Similarity NPC19305
0.7222 Intermediate Similarity NPC149821
0.7222 Intermediate Similarity NPC5413
0.7222 Intermediate Similarity NPC163345
0.7167 Intermediate Similarity NPC474267
0.7167 Intermediate Similarity NPC106851
0.7167 Intermediate Similarity NPC274927
0.7143 Intermediate Similarity NPC31551
0.7143 Intermediate Similarity NPC219536
0.7115 Intermediate Similarity NPC8219
0.7091 Intermediate Similarity NPC301482
0.7091 Intermediate Similarity NPC59051
0.7069 Intermediate Similarity NPC45626
0.7069 Intermediate Similarity NPC52264
0.7059 Intermediate Similarity NPC236579
0.7059 Intermediate Similarity NPC203531
0.7049 Intermediate Similarity NPC251042
0.7049 Intermediate Similarity NPC299730
0.7049 Intermediate Similarity NPC122521
0.7049 Intermediate Similarity NPC174447
0.7037 Intermediate Similarity NPC207292
0.7015 Intermediate Similarity NPC186531
0.7 Intermediate Similarity NPC165533
0.7 Intermediate Similarity NPC12156
0.7 Intermediate Similarity NPC149299
0.7 Intermediate Similarity NPC329819
0.7 Intermediate Similarity NPC40597
0.7 Intermediate Similarity NPC250028
0.7 Intermediate Similarity NPC256163
0.6981 Remote Similarity NPC172042
0.6935 Remote Similarity NPC40082
0.6935 Remote Similarity NPC328776
0.6935 Remote Similarity NPC271282
0.6935 Remote Similarity NPC325929
0.6935 Remote Similarity NPC66460
0.6935 Remote Similarity NPC477829
0.6935 Remote Similarity NPC320305
0.6923 Remote Similarity NPC271921
0.6923 Remote Similarity NPC330426
0.6923 Remote Similarity NPC473829
0.6923 Remote Similarity NPC148192
0.6923 Remote Similarity NPC22101
0.6923 Remote Similarity NPC127091
0.6923 Remote Similarity NPC475443
0.6923 Remote Similarity NPC104537
0.6909 Remote Similarity NPC473551
0.6909 Remote Similarity NPC304162
0.6897 Remote Similarity NPC137538
0.6875 Remote Similarity NPC318420
0.6875 Remote Similarity NPC136164
0.6875 Remote Similarity NPC326268
0.6875 Remote Similarity NPC255863
0.6875 Remote Similarity NPC245947
0.6863 Remote Similarity NPC53541
0.6863 Remote Similarity NPC163746
0.6863 Remote Similarity NPC103286
0.6852 Remote Similarity NPC42304
0.6842 Remote Similarity NPC216407
0.6842 Remote Similarity NPC129458
0.6825 Remote Similarity NPC29697
0.6818 Remote Similarity NPC218477
0.6818 Remote Similarity NPC473559
0.6818 Remote Similarity NPC324981
0.6818 Remote Similarity NPC48218
0.6818 Remote Similarity NPC141481
0.68 Remote Similarity NPC80234
0.68 Remote Similarity NPC223249
0.6792 Remote Similarity NPC47363
0.6792 Remote Similarity NPC287231
0.6786 Remote Similarity NPC474391
0.6769 Remote Similarity NPC126899
0.6769 Remote Similarity NPC304665
0.6769 Remote Similarity NPC477982
0.6769 Remote Similarity NPC154728
0.6731 Remote Similarity NPC71317
0.6731 Remote Similarity NPC301528
0.6731 Remote Similarity NPC129972
0.6727 Remote Similarity NPC91495
0.6724 Remote Similarity NPC10081
0.6724 Remote Similarity NPC225066
0.6721 Remote Similarity NPC34416
0.6716 Remote Similarity NPC473772
0.6716 Remote Similarity NPC317583
0.6714 Remote Similarity NPC81052
0.6667 Remote Similarity NPC239754
0.6667 Remote Similarity NPC125312
0.6667 Remote Similarity NPC48930
0.6667 Remote Similarity NPC30195
0.6667 Remote Similarity NPC12438
0.6667 Remote Similarity NPC117572
0.6667 Remote Similarity NPC156630
0.6667 Remote Similarity NPC99619
0.6667 Remote Similarity NPC174560
0.6667 Remote Similarity NPC321838
0.6667 Remote Similarity NPC26500
0.6618 Remote Similarity NPC42526
0.6618 Remote Similarity NPC476660
0.661 Remote Similarity NPC269615
0.661 Remote Similarity NPC87394
0.6604 Remote Similarity NPC317128
0.6567 Remote Similarity NPC477980
0.6552 Remote Similarity NPC303765
0.6552 Remote Similarity NPC473705
0.6552 Remote Similarity NPC236872
0.6545 Remote Similarity NPC474204
0.6545 Remote Similarity NPC110234
0.6545 Remote Similarity NPC44363
0.6545 Remote Similarity NPC163751
0.6538 Remote Similarity NPC149184
0.6538 Remote Similarity NPC196924
0.6538 Remote Similarity NPC307783
0.6538 Remote Similarity NPC171736
0.6538 Remote Similarity NPC216630
0.6538 Remote Similarity NPC209970
0.6491 Remote Similarity NPC142103
0.6486 Remote Similarity NPC200446
0.6471 Remote Similarity NPC143396
0.6471 Remote Similarity NPC113928
0.6471 Remote Similarity NPC301696
0.6471 Remote Similarity NPC154186
0.6471 Remote Similarity NPC261080
0.6471 Remote Similarity NPC301585
0.6471 Remote Similarity NPC201844
0.6471 Remote Similarity NPC14227
0.6471 Remote Similarity NPC279026
0.6471 Remote Similarity NPC199557
0.6438 Remote Similarity NPC469495
0.6429 Remote Similarity NPC106872

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC161366 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8269 Intermediate Similarity NPD28 Approved
0.8269 Intermediate Similarity NPD29 Approved
0.8039 Intermediate Similarity NPD622 Approved
0.7963 Intermediate Similarity NPD3172 Approved
0.7818 Intermediate Similarity NPD3196 Approved
0.7818 Intermediate Similarity NPD4266 Approved
0.7818 Intermediate Similarity NPD3195 Phase 2
0.7818 Intermediate Similarity NPD3194 Approved
0.7647 Intermediate Similarity NPD3174 Discontinued
0.7222 Intermediate Similarity NPD3173 Approved
0.7037 Intermediate Similarity NPD5343 Approved
0.6984 Remote Similarity NPD3197 Phase 1
0.6939 Remote Similarity NPD3206 Approved
0.6792 Remote Similarity NPD2699 Approved
0.6667 Remote Similarity NPD4222 Approved
0.6538 Remote Similarity NPD2270 Approved
0.6481 Remote Similarity NPD6097 Approved
0.6481 Remote Similarity NPD6096 Approved
0.6471 Remote Similarity NPD9448 Phase 2
0.6471 Remote Similarity NPD633 Phase 3
0.6364 Remote Similarity NPD39 Approved
0.6269 Remote Similarity NPD6108 Clinical (unspecified phase)
0.625 Remote Similarity NPD4246 Clinical (unspecified phase)
0.625 Remote Similarity NPD8039 Approved
0.6182 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6154 Remote Similarity NPD9655 Approved
0.614 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6111 Remote Similarity NPD387 Clinical (unspecified phase)
0.6 Remote Similarity NPD5326 Phase 3
0.5867 Remote Similarity NPD4756 Discovery
0.5833 Remote Similarity NPD6927 Phase 3
0.5806 Remote Similarity NPD3728 Approved
0.5806 Remote Similarity NPD3730 Approved
0.5789 Remote Similarity NPD634 Phase 3
0.5789 Remote Similarity NPD3732 Approved
0.5769 Remote Similarity NPD5369 Approved
0.5714 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5696 Remote Similarity NPD6435 Approved
0.5692 Remote Similarity NPD6109 Phase 1
0.5641 Remote Similarity NPD5368 Approved
0.5625 Remote Similarity NPD5362 Discontinued
0.5625 Remote Similarity NPD5332 Approved
0.5625 Remote Similarity NPD5331 Approved
0.5625 Remote Similarity NPD7154 Phase 3

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data